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Changelog

Source: NEWS.md

bHIVE 0.99.2

Breaking Changes

  • Removed regression task support across the package. The previous regression implementation was unreliable and is being redesigned. bHIVE(), honeycombHIVE(), swarmbHIVE(), refineB(), AINet, GerminalCenter, bHIVEmodel, honeycombHIVEmodel, and visualizeHIVE() no longer accept task = "regression" or numeric y.
  • Removed regression-only loss functions (mse, huber, poisson) and regression metrics (rmse, mae, r2) from swarmbHIVE().
  • Removed refineHuberDelta parameter from honeycombHIVE() and honeycombHIVEmodel.
  • final_assignment_cpp() no longer accepts antibody_values or overall_mean arguments.

bHIVE 0.99.1

C++ Backend

  • Added RcppArmadillo backend for BLAS-optimized bulk affinity and distance matrix computation, replacing per-element R loops
  • Scalar affinity function for clone/mutate hot path avoids 1x1 matrix allocation overhead
  • C++ implementations for clonal selection iteration, network suppression, kmeans++ initialization, final assignment, somatic hypermutation (5 methods), and idiotypic network dynamics

R6 Class Architecture

  • New ImmuneRepertoire class for antibody collections with metadata tracking (isotype, state, age, lineage)
  • New ImmuneAlgorithm abstract base class with fit/predict/summary interface
  • New AINet class wrapping core algorithm with composable module injection
  • Both R6 composition and functional API equally supported

New Modules

  • SHMEngine — Five somatic hypermutation strategies: uniform (original behavior), airs (affinity-proportional), hotspot (feature-gradient-weighted), energy (budget-constrained), and adaptive (per-feature Adam-like moment tracking)
  • IdiotypicNetwork — Antibody-antibody network dynamics with bell-shaped activation function replacing epsilon-threshold suppression
  • GerminalCenter — T-follicular helper mediated selection with task-aware quality scoring and resource competition
  • Microenvironment — Density-dependent zone classification (stable/explore/boundary) with chemokine-like gradient computation
  • VDJLibrary — Combinatorial V(D)J gene library initialization via PCA, k-means clustering, or random partition of feature space
  • ActivationGate — Two-signal activation gate requiring both antigen recognition and costimulatory context (density, danger, or entropy)
  • MemoryPool — Archive high-affinity antibodies as long-lived memory cells with threshold-based recall
  • ClassSwitcher — Isotype class switching (IgM broad, IgG specific, IgA boundary) modulating effective kernel width
  • ConvergentSelector — Cross-repertoire consensus identification of public antibodies for ensemble methods

Documentation

  • Complete README rewrite covering functional API, R6 API, module reference table, and architecture overview
  • New pkgdown website with Bootstrap 5 Flatly theme, organized reference groups, and tutorial navigation
  • New article: “Composing Immune Modules” — R6 composition patterns for all 9 modules with worked examples
  • New article: “Advanced Tuning & Workflows” — swarmbHIVE grid search, honeycombHIVE multilayer refinement, refineB optimizer comparison, caret integration, and visualizeHIVE plot types
  • New article: “Algorithm & Biological Foundations” — comprehensive mathematical reference covering all affinity kernels, distance functions, SHM strategies, idiotypic ODE system, germinal center selection, and parameter guidance
  • Added roxygen @examples to refineB, bHIVEmodel, and ImmuneAlgorithm (now 90% example coverage)
  • GitHub Actions workflow for automated pkgdown deployment to borch.dev

Package Infrastructure

  • Created R/bHIVE-package.R with roxygen-managed @useDynLib and @importFrom Rcpp sourceCpp directives
  • Added %||% operator @name null-coalesce to avoid illegal characters in Rd \name field
  • Moved tutorial vignettes to vignettes/articles/ (pkgdown-only, not installed with package) to reduce installed size
  • Added pkgdown configuration (_pkgdown.yml) with 7 reference groups and structured article hierarchy

Testing

  • Added comprehensive unit tests for all 12 R6 module classes (ImmuneRepertoire, ImmuneAlgorithm, AINet, SHMEngine, IdiotypicNetwork, GerminalCenter, Microenvironment, VDJLibrary, ActivationGate, MemoryPool, ClassSwitcher, ConvergentSelector) and C++ backend functions
  • Test coverage increased from ~26% to ~85% (681 tests, 0 failures)

BiocCheck Compliance

  • Replaced all sapply() calls with vapply() in bHiVE.R and visualizeHIVE.R
  • Replaced all 1:n patterns with seq_len() / seq_along()
  • Removed install.packages() calls from vignettes
  • Removed LazyData: true from DESCRIPTION
  • Updated R dependency to >= 4.5.0
  • Updated biocViews to Software, Clustering, Classification, Regression, Network
  • Added class-level @param documentation for all R6 initialize() arguments across 11 module classes
  • Added @param ... Not used. to all R6 print() methods

Bug Fixes

  • Fixed kmeans++ sampling: corrected cumulative sum fallback index and runif-to-integer cast
  • Fixed cosine similarity epsilon (1e-12) for numerical stability
  • Fixed division-by-zero guard in idiotypic dynamics when theta_low equals theta_high
  • Fixed VDJLibrary NaN in kmeans for single-allele edge cases
  • Fixed VDJLibrary NA subscript when feature dimensions not divisible by 3
  • Removed duplicate Classification from biocViews, added Clustering
  • Fixed vignette YAML parsing error from bare --- horizontal rule

bHIVE 0.99.0

  • Initial submission version with core AIS functionality
  • Clonal selection, network suppression, and mutation for clustering, classification, and regression
  • honeycombHIVE multilayer architecture
  • swarmbHIVE hyperparameter tuning via BiocParallel
  • caret model integration (bHIVEmodel, honeycombHIVEmodel)
  • Visualization utilities via ggplot2